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3397 (A > G)

General info

Mitimpact ID
MI.10948
Chr
chrM
Start
3397
Ref
A
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
91
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATA/GTA
AA pos
31
AA ref
M
AA alt
V
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3397A>G
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Conservation

PhyloP 100v
8.729 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.036 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Likely benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
Disease Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
9726
Clinvar ALLELEID
24765
Clinvar CLNDISDB
Mondo:mondo:0008199, medgen:c3160718, omim:168600, orphanet:411602;

human phenotype ontology:hp:0002511, human phenotype ontology:hp:0006878, human phenotype ontology:hp:0007213, mondo:mondo:0004975, medgen:c0002395, orphanet:1020;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Parkinson disease, late-onset;

alzheimer disease;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
3397A>G
MITOMAP Disease Clinical info
Adpd / possibly lvnc-cardiomyopathy associated / resistance to high altitude pulmonary edema
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.2748%
MITOMAP General GenBank Seqs
168
MITOMAP General GenBank Curated refs
22312186 8741876 17637808 8104867 21263444 18477584 20211276 15972314 29987491 7599217 16523671 15638829 12406974 21457906 22487888 19043581 27498855 19703591
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56427
Gnomad AC hom
85
Gnomad AF hom
0.0015063
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
464
HelixMTdb AF hom
0.0023675
HelixMTdb AC het
9
HelixMTdb AF het
4.59e-05
HelixMTdb mean ARF
0.5238
HelixMTdb max ARF
0.90698
ToMMo JPN54K AC
46
ToMMo JPN54K AF
0.000847
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

3397 (A > C)

General info

Mitimpact ID
MI.10949
Chr
chrM
Start
3397
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
91
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATA/CTA
AA pos
31
AA ref
M
AA alt
L
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3397A>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Powered by MitoWheel

Conservation

PhyloP 100v
8.729 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.036 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
3397A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

3397 (A > T)

General info

Mitimpact ID
MI.10947
Chr
chrM
Start
3397
Ref
A
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
91
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ATA/TTA
AA pos
31
AA ref
M
AA alt
L
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3397A>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
8.729 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.036 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
3397A>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 3397 (A/G) 3397 (A/C) 3397 (A/T)
~ 3397 (ATA/GTA) 3397 (ATA/CTA) 3397 (ATA/TTA)
MitImpact id MI.10948 MI.10949 MI.10947
Chr chrM chrM chrM
Start 3397 3397 3397
Ref A A A
Alt G C T
Gene symbol MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 91 91 91
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution ATA/GTA ATA/CTA ATA/TTA
AA position 31 31 31
AA ref M M M
AA alt V L L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3397A>G NC_012920.1:g.3397A>C NC_012920.1:g.3397A>T
HGNC id 7455 7455 7455
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 8.729 8.729 8.729
PhyloP 470Way 0.58 0.58 0.58
PhastCons 100V 1 1 1
PhastCons 470Way 0.036 0.036 0.036
PolyPhen2 benign benign benign
PolyPhen2 score 0.32 0.23 0.23
SIFT neutral neutral neutral
SIFT score 0.41 0.46 0.46
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.007 0.002 0.002
VEST Neutral Neutral Neutral
VEST pvalue 0.15 0.15 0.15
VEST FDR 0.4 0.4 0.4
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.84 0.7 0.7
MutationTaster . . .
MutationTaster score . . .
MutationTaster converted rankscore . . .
MutationTaster model . . .
MutationTaster AAE . . .
fathmm . . .
fathmm score . . .
fathmm converted rankscore . . .
AlphaMissense likely_benign ambiguous ambiguous
AlphaMissense score 0.2561 0.3849 0.3849
CADD Neutral Neutral Neutral
CADD score 0.63201 1.181688 1.214899
CADD phred 8.375 11.65 11.83
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.49 -2.64 -2.64
MutationAssessor medium medium medium
MutationAssessor score 2.385 2.785 2.785
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.248 0.548 0.548
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.458 0.434 0.434
MLC Neutral Neutral Neutral
MLC score 0.12242742 0.12242742 0.12242742
PANTHER score . . .
PhD-SNP score 0.837 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.94 0.34 0.34
APOGEE2 VUS+ VUS+ VUS+
APOGEE2 score 0.685938855708491 0.565130479391109 0.565128309849472
CAROL neutral neutral neutral
CAROL score 0.51 0.44 0.44
Condel deleterious deleterious deleterious
Condel score 0.55 0.62 0.62
COVEC WMV neutral neutral neutral
COVEC WMV score -3 -3 -3
MtoolBox neutral neutral neutral
MtoolBox DS 0.42 0.36 0.36
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP Disease . .
Meta-SNP score 0.694 . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score -0.44 -0.26 -0.26
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.19 0.24 0.24
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.88 1.16 1.16
CHASM Neutral Neutral Neutral
CHASM pvalue 0.41 0.42 0.42
CHASM FDR 0.8 0.8 0.8
ClinVar id 9726.0 . .
ClinVar Allele id 24765.0 . .
ClinVar CLNDISDB MONDO:MONDO:0008199,MedGen:C3160718,OMIM:168600,Orphanet:411602|Human_Phenotype_Ontology:HP:0002511,Human_Phenotype_Ontology:HP:0006878,Human_Phenotype_Ontology:HP:0007213,MONDO:MONDO:0004975,MedGen:C0002395,Orphanet:1020|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Parkinson_disease,_late-onset|Alzheimer_disease|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info ADPD / possibly LVNC-cardiomyopathy associated / resistance to high altitude pulmonary edema . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.2748% . .
MITOMAP General GenBank Seqs 168 . .
MITOMAP General Curated refs 22312186;8741876;17637808;8104867;21263444;18477584;20211276;15972314;29987491;7599217;16523671;15638829;12406974;21457906;22487888;19043581;27498855;19703591 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56427.0 . .
gnomAD 3.1 AC Homo 85.0 . .
gnomAD 3.1 AF Hom 0.00150637 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.7722e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 464.0 . .
HelixMTdb AF Hom 0.0023675524 . .
HelixMTdb AC Het 9.0 . .
HelixMTdb AF Het 4.5922352e-05 . .
HelixMTdb mean ARF 0.5238 . .
HelixMTdb max ARF 0.90698 . .
ToMMo 54KJPN AC 46 . .
ToMMo 54KJPN AF 0.000847 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id . . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
0
Details:
0
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min -20, max 12]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.15
  • Possibly damaging:  0.15 < score <= 0.85
  • Probably damaging:  score > 0.85
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -16.13, max 10.64]
  • Neutral:  score > 1.5
  • Deleterious:  score <= 1.5
Score:  
0
  [min 0.0, max 1.0]
  • Likely benign:  score <= 0.34
  • Ambiguous:  0.34 < score < 0.56
  • Likely pathogenic:  score >= 0.56
Score:  
0
  [min -14, max 14]
  • Neutral:  score > -2.5
  • Deleterious:  score <= -2.5 (soft threshold)
Score:  
0
  [min -6, max 6]
  • Neutral:  score <= 0.8
  • Low impact:  0.8 < score <= 1.9
  • Medium impact:  1.9 < score <= 3.5
  • High impact:  score > 3.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.6
  • Damaging:  score <= 0.6
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.28
  • Damaging:  score <= 0.28
Phred score:  
0
  [min 0, max Unlimited]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5 (soft threshold)
  • Deleterious:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Polymorphism:  score < 0.5
  • Disease causing:  score >= 0.5
P-value:  
0
  [min 0, max 1]
  • Neutral:  p-value > 0.05
  • Pathogenic:  p-value <= 0.05
Score:  
0
  [min 0, max 1]
No hard-thresholds were indicated by authors (ref). Indicatively:
  • Neutral:  score < 0.9
  • Pathogenic:  score >= 0.9
No score. Categorical only
Please refer to Additional File 14: Table S10 for further details.
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.98
  • Deleterious:  score >= 0.98
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
Score:  
0
  [min -6, max 6]
  • Neutral:  score < 0
  • Deleterious:  score > 0
  • Inaccurate prediction:  score = 0
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
DS score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.43
  • Deleterious:  score >= 0.43
Pathogenicity score:  
0
  [min 0, max 1]
  • Neutral:  score ≤ 0.5
  • Pathogenic:  score > 0.5


Pathogenicity score for this variant:  
0
  [min 0, max 1]
ACMG-AMP curations for mitochondrial variants should use the raw scores. Standalone probabilities are shown below:
  • Benign:  score ≤ 0.062 (prob. ≤ 0.001)
  • Likely-benign:  0.062 < score ≤ 0.265 (0.001 < prob. ≤ 0.1)
  • Low-scoring VUS (VUS-):  0.265 < score ≤ 0.396 (0.1 < prob. ≤ 0.33)
  • VUS:  0.396 < score ≤ 0.544 (0.33 < prob. ≤ 0.66)
  • High-scoring VUS (VUS+):  0.544 < score < 0.716 (0.66 < prob. < 0.9)
  • Likely-pathogenic:  0.716 ≤ score < 0.907 (0.9 ≤ prob. < 0.99)
  • Pathogenic:  score ≥ 0.907 (prob. ≥ 0.99)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1 (soft threshold)
  • Medium impact:  -1 < score < 1.5 (soft threshold)
  • High impact:  score >= 1.5 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
P-value:  
0
  [min 0, max 1]
  • Neutral:  FDR > 0.2
  • Driver:  FDR <= 0.2
The frequency of a CPD variant is proportional to the
number of aligned orthologous sequences that
carry a specific human pathogenic variant as
wild-type amino acid on the total number of aligned
sequences.

For more info, please check the output legend